Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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siMacro: A Fast and Easy Data Processing Tool for Cell-Based Genomewide siRNA Screens

  • Singh, Nitin Kumar (Department of Bioengineering, University of Texas at Dallas) ;
  • Seo, Bo Yeun (Department of Cell Biology, University of Texas Southwestern Medical Center) ;
  • Vidyasagar, Mathukumalli (Department of Bioengineering, University of Texas at Dallas) ;
  • White, Michael A. (Department of Cell Biology, University of Texas Southwestern Medical Center) ;
  • Kim, Hyun Seok (Department of Cell Biology, University of Texas Southwestern Medical Center)
  • Received : 2012.12.05
  • Accepted : 2013.01.18
  • Published : 2013.03.31
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Abstract

Growing numbers of studies employ cell line-based systematic short interfering RNA (siRNA) screens to study gene functions and to identify drug targets. As multiple sources of variations that are unique to siRNA screens exist, there is a growing demand for a computational tool that generates normalized values and standardized scores. However, only a few tools have been available so far with limited usability. Here, we present siMacro, a fast and easy-to-use Microsoft Office Excel-based tool with a graphic user interface, designed to process single-condition or two-condition synthetic screen datasets. siMacro normalizes position and batch effects, censors outlier samples, and calculates Z-scores and robust Z-scores, with a spreadsheet output of >120,000 samples in under 1 minute.

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References

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